This exercise is from the Core Skills section on Muting.
Funk muting is about rhythm and control. Use the fretboard thumb to mute strings from over the topside of the fretboard again. Mute from whichever fret is comfortable, you aren't playing notes with your thumb - so just as long as these strings are deadened. Remember not to sound out harmonics around the 7th and 9th frets with your thumb.
The timing and rhythm are important, so pay close attention to maintaining these with your strumming hand. If the tune is tricky, try working at it bit-by-bit until you can piece it all together in sequence.
There is a nice long normal speed version for you to practice along with. Playing along with it will help you get up to speed and maintain timing. Also try layering your own riffs and melodies along with it for more fun.
This time we're using some other techniques (bending) and the licks are a little more complicated.
The tune starts with a little lick using notes from an E natural minor scale. There is a muted E minor chord during this lick, which is repeated twice. Then play E major (played in a half G shape position from fret 9), and A major (D shape position 9). There is a little sus 4 added to the A major with your little finger before repeating again from the E major chord.